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VariantGenomicLocationAssociationDTO

None

classDiagram VariantLocationAssociationDTO <|-- VariantGenomicLocationAssociationDTO VariantGenomicLocationAssociationDTO : chromosome_curie VariantGenomicLocationAssociationDTO : consequence_curie VariantGenomicLocationAssociationDTO : created_by_curie VariantGenomicLocationAssociationDTO : curated_consequence_curie VariantGenomicLocationAssociationDTO : date_created VariantGenomicLocationAssociationDTO : date_updated VariantGenomicLocationAssociationDTO : db_date_created VariantGenomicLocationAssociationDTO : db_date_updated VariantGenomicLocationAssociationDTO : deleted_sequence VariantGenomicLocationAssociationDTO : dna_mutation_type_curie VariantGenomicLocationAssociationDTO : end VariantGenomicLocationAssociationDTO : evidence_curies VariantGenomicLocationAssociationDTO : gene_localization_type_curie VariantGenomicLocationAssociationDTO : inserted_sequence VariantGenomicLocationAssociationDTO : internal VariantGenomicLocationAssociationDTO : number_additional_dna_base_pairs VariantGenomicLocationAssociationDTO : number_removed_dna_base_pairs VariantGenomicLocationAssociationDTO : obsolete VariantGenomicLocationAssociationDTO : padded_base VariantGenomicLocationAssociationDTO : reference_sequence VariantGenomicLocationAssociationDTO : relation_name VariantGenomicLocationAssociationDTO : start VariantGenomicLocationAssociationDTO : updated_by_curie VariantGenomicLocationAssociationDTO : variant_identifier VariantGenomicLocationAssociationDTO : variant_sequence VariantGenomicLocationAssociationDTO : variation_strand

URI: alliance:VariantGenomicLocationAssociationDTO

Parent Classes

Children

Slots

Name Description
chromosome_curie The NCBI chromosome accession number for the chromosome.
consequence_curie Curie of SOTerm (child of SO:0001576 - transcript_variant) that describes the consequence of the variant, as stated in the source reference. In practice source consequence will be associated with locations at any or all of VariantLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
created_by_curie Curie of the Person object representing the individual that created the entity
curated_consequence_curie Curie of SOTerm that describes the consequence of the variant, as determined by the curator. In practice curated consequence will be associated with locations at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
date_created The date on which an entity was created. This can be applied to nodes or edges.
date_updated Date on which an entity was last modified.
db_date_created The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
deleted_sequence The sequence of DNA base pairs removed from the reference sequence by the variant.
dna_mutation_type_curie Curie of SOTerm describing the type of DNA mutation, for example, insertion, deletion, substitution, or indel.
end The end of the feature in positive 1-based integer coordinates relative to the reference landmark.
evidence_curies Curies of InformationContentEntity objects given as evidence
gene_localization_type_curie Curie of SOTerm describing the type of gene localization, for example, intronic, intergenic, or intragenic.
inserted_sequence The sequence of DNA base pairs inserted into the reference sequence by the variant.
internal Classifies the entity as private (for internal use) or not (for public use).
number_additional_dna_base_pairs The number of additional DNA base pairs inserted into the reference sequence by the variant.
number_removed_dna_base_pairs The number of DNA base pairs removed from the reference sequence by the variant. sequence.
obsolete Entity is no longer current.
padded_base A base preceded an insertion or deletion event that is reported when either the reference or variant sequence would otherwise be empty.
reference_sequence Reference sequence of genome or genomic entity at position of aligned variant.
relation_name Name of VocabularyTerm representing relation of an Association
start The start of the feature in positive 1-based integer coordinates relative to the reference landmark.
updated_by_curie Curie of the Person object representing the individual that updated the entity
variant_identifier Identifier (curie/primary_external_id/mod_internal_id) of the variant
variant_sequence Sequence that differs from the reference sequence of genome or genomic entity at position of variant, as specified by curator.
variation_strand The strand on which the variant is located. This is the strand of the reference sequence, not the variant sequence.

Mappings

Mapping Type Mapped Value
self ['alliance:VariantGenomicLocationAssociationDTO']
native ['alliance:VariantGenomicLocationAssociationDTO']

LinkML Specification

Direct

name: VariantGenomicLocationAssociationDTO
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantLocationAssociationDTO
abstract: true
slots:
- chromosome_curie
- variation_strand
- number_additional_dna_base_pairs
- number_removed_dna_base_pairs
- inserted_sequence
- deleted_sequence
- padded_base
- dna_mutation_type_curie
- gene_localization_type_curie

Induced

name: VariantGenomicLocationAssociationDTO
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: VariantLocationAssociationDTO
abstract: true
attributes:
  chromosome_curie:
    name: chromosome_curie
    description: The NCBI chromosome accession number for the chromosome.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: chromosome_curie
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    range: string
    required: true
  variation_strand:
    name: variation_strand
    description: The strand on which the variant is located.  This is the strand of
      the reference sequence, not the variant sequence.
    notes:
    - 'QUESTION: I thought that the agreed upon convention was to report the reference
      sequence relative to the + strand of the scaffold, making this redundant and
      potentially confusing. (Gil)'
    examples:
    - value: +
    - value: '-'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: variation_strand
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
    required: false
  number_additional_dna_base_pairs:
    name: number_additional_dna_base_pairs
    description: The number of additional DNA base pairs inserted into the reference
      sequence by the variant.
    examples:
    - value: '1'
    - value: '2'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: number_additional_dna_base_pairs
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: integer
    required: false
  number_removed_dna_base_pairs:
    name: number_removed_dna_base_pairs
    description: The number of DNA base pairs removed from the reference sequence
      by the variant.   sequence.
    examples:
    - value: '1'
    - value: '2'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: number_removed_dna_base_pairs
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: integer
    required: false
  inserted_sequence:
    name: inserted_sequence
    description: The sequence of DNA base pairs inserted into the reference sequence
      by the variant.
    examples:
    - value: A
    - value: AT
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: inserted_sequence
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
    required: false
  deleted_sequence:
    name: deleted_sequence
    description: The sequence of DNA base pairs removed from the reference sequence
      by the variant.
    examples:
    - value: A
    - value: AT
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: deleted_sequence
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
    required: false
  padded_base:
    name: padded_base
    description: 'A base preceded an insertion or deletion event that is reported
      when either the reference or variant sequence would otherwise be empty. '
    examples:
    - value: A
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: padded_base
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    - VariantGenomicLocationAssociation
    range: string
  dna_mutation_type_curie:
    name: dna_mutation_type_curie
    description: Curie of SOTerm describing the type of DNA mutation, for example,
      insertion, deletion, substitution, or indel.
    notes:
    - This is a ZFIN specific field.
    examples:
    - value: SO:1000027
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: dna_mutation_type_curie
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    range: SOTerm
  gene_localization_type_curie:
    name: gene_localization_type_curie
    description: Curie of SOTerm describing the type of gene localization, for example,
      intronic, intergenic, or intragenic.
    examples:
    - value: SO:0000147
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: gene_localization_type_curie
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantGenomicLocationAssociationDTO
    range: string
  variant_identifier:
    name: variant_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of the variant
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: genomic_entity_identifier
    alias: variant_identifier
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    - AlleleVariantAssociationDTO
    range: string
    required: true
  reference_sequence:
    name: reference_sequence
    description: Reference sequence of genome or genomic entity at position of aligned
      variant.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociation
    multivalued: false
    alias: reference_sequence
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    - VariantLocationAssociation
    range: biological_sequence
    required: false
  variant_sequence:
    name: variant_sequence
    description: Sequence that differs from the reference sequence of genome or genomic
      entity at position of variant, as specified by curator.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociation
    multivalued: false
    alias: variant_sequence
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    - VariantLocationAssociation
    range: biological_sequence
    required: false
  consequence_curie:
    name: consequence_curie
    description: Curie of SOTerm (child of SO:0001576 - transcript_variant) that describes
      the consequence of the variant, as stated in the source reference. In practice
      source consequence will be associated with locations at any or all of VariantLocationAssociation,
      VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociationDTO
    multivalued: false
    alias: consequence_curie
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    range: string
    required: false
  curated_consequence_curie:
    name: curated_consequence_curie
    description: Curie of SOTerm that describes the consequence of the variant, as
      determined by the curator. In practice curated consequence will be associated
      with locations at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation,
      and VariantPolypeptideLocationAssociation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: VariantLocationAssociationDTO
    multivalued: false
    alias: curated_consequence_curie
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - VariantLocationAssociationDTO
    range: string
    required: false
  relation_name:
    name: relation_name
    description: Name of VocabularyTerm representing relation of an Association
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: relation_name
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - SequenceTargetingReagentGeneAssociationDTO
    - AlleleCellLineAssociationDTO
    - AlleleGenerationMethodAssociationDTO
    - AlleleGenomicEntityAssociationDTO
    - AlleleImageAssociationDTO
    - AlleleOriginAssociationDTO
    - ConstructComponentSlotAnnotationDTO
    - LocationAssociationDTO
    range: string
    required: true
    any_of:
    - equals_string: has_location
  start:
    name: start
    description: The start of the feature in positive 1-based integer coordinates
      relative to the reference landmark.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: LocationAssociation
    alias: start
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
  end:
    name: end
    description: The end of the feature in positive 1-based integer coordinates relative
      to the reference landmark.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: LocationAssociation
    alias: end
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - LocationAssociation
    - LocationAssociationDTO
    range: integer
  evidence_curies:
    name: evidence_curies
    description: Curies of InformationContentEntity objects given as evidence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence_curies
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - NoteDTO
    - SlotAnnotationDTO
    - EvidenceAssociationDTO
    - GeneGeneAssociationDTO
    range: string
  created_by_curie:
    name: created_by_curie
    description: Curie of the Person object representing the individual that created
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: created_by_curie
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by_curie:
    name: updated_by_curie
    description: Curie of the Person object representing the individual that updated
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: updated_by_curie
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: VariantGenomicLocationAssociationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean